1. Are you saying that the Koran does not command the killing of "infidels"? That it is merely passages taken out of context?
Well, duh. I'm not a Muslim, and I know that much. The Koran has a lot of passages about fighting wars with enemies of Islam, who were a combination of pagans, Christians and Jews. However, it also has passages about treating Christians and Jews fairly and allowing them practice their religions, and passages stating that they can achieve salvation (or whatever the Islamic equivalent, not sure here). And more generally, it has passages about not picking fights with people who don't pick fights with you.
So, well, the straightforward conclusion here is that the Koran says a lot of different things about the relationship between Muslims and non-Muslims, and that the context in which each of those things is said needs to be weighed to see which of them best match any given situation. As, well, every single damn book ever written to guide human behavior.
PS: Muslims do not generally consider Christians and Jews to be "infidels." Rather, they consider them to be people who believe in the same god as Muslims, received the same teachings that Mohammed did, but then lost or distorted them. You will of course find plenty of counterexamples to this rule—"Christian = infidel" is an Islamist terrorist theme—but it's by no means a majority opinion. So I'm not interested in responses that document Muslims who have labeled Christians as "infidels"—I know they exist, and I know it's a minority opinion.
PPS: The fact the the Koran periodically has nice things to say about non-Muslims doesn't mean that all Muslims in general will have a good opinion of Christians and Jews; I'm not interested in responses that document cases of Muslims saying bad things about non-Muslims, mistreating them or showing prejudices toward them. In fact, the Koran's nicer statements about non-Muslims often seem like attempts to correct early Muslims' pre-existing prejudices and ill will against them. Take, for example, the Koran's statement that the food of the Peoples of the Book (Christians and Jews) is OK for Muslims to eat. Why would such a rule need to be stated? Well, some early Muslims must have seen some forms of physical contact with Christians as taboo. Similar comments apply where it says that you should not fight or kill non-Muslims who haven't tried to do the same to you: "Don't kill Christians and Jews" must have been a teaching that needed to be taught in Mohammed's time as much as in ours. Religion exists in a harsh, often brutal world of people who adopt it more as a tribal identity than as a moral guide.